AutoCloner

Multiple sequence alignment - TraesCS1A01G300600

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)

BLAST Results

Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

	qseqid	sseqid	percentage.identical	alignment.length	no.mismatch	no.gap.openings	qstart	qend	sstart	send	evalue	bitscore
0	TraesCS1A01G300600	chr1A	100.000	2730	0	0	1	2730	495331315	495334044	0.000000e+00	5042.0
1	TraesCS1A01G300600	chr1A	95.918	49	2	0	823	871	495319951	495319999	2.250000e-11	80.5
2	TraesCS1A01G300600	chr1D	91.223	1880	113	27	886	2730	398379575	398381437	0.000000e+00	2510.0
3	TraesCS1A01G300600	chr1D	82.229	951	112	33	829	1765	398246033	398246940	0.000000e+00	767.0
4	TraesCS1A01G300600	chr1D	83.544	790	91	20	889	1662	398121325	398122091	0.000000e+00	702.0
5	TraesCS1A01G300600	chr1D	84.036	664	78	16	1116	1765	398093760	398094409	5.000000e-172	614.0
6	TraesCS1A01G300600	chr1B	89.418	1805	129	28	942	2720	533815167	533816935	0.000000e+00	2218.0
7	TraesCS1A01G300600	chr1B	94.139	836	43	5	1	831	26840609	26839775	0.000000e+00	1267.0
8	TraesCS1A01G300600	chr1B	82.772	801	86	29	973	1763	533759781	533760539	0.000000e+00	667.0
9	TraesCS1A01G300600	chr1B	83.287	712	84	21	1112	1804	533747815	533748510	8.300000e-175	623.0
10	TraesCS1A01G300600	chr7A	95.066	831	36	4	1	827	594889133	594889962	0.000000e+00	1303.0
11	TraesCS1A01G300600	chr7A	94.952	832	37	4	1	828	276128463	276127633	0.000000e+00	1299.0
12	TraesCS1A01G300600	chr7A	94.498	836	41	4	1	833	705060202	705061035	0.000000e+00	1284.0
13	TraesCS1A01G300600	chr7A	94.565	828	41	4	1	825	689969606	689968780	0.000000e+00	1277.0
14	TraesCS1A01G300600	chr2A	94.718	833	37	7	1	828	319017776	319016946	0.000000e+00	1288.0
15	TraesCS1A01G300600	chr2A	94.572	829	40	4	1	825	621443302	621444129	0.000000e+00	1277.0
16	TraesCS1A01G300600	chr3A	94.478	833	40	5	1	828	649849367	649848536	0.000000e+00	1279.0
17	TraesCS1A01G300600	chr6A	94.451	829	40	5	1	825	93181219	93180393	0.000000e+00	1271.0
18	TraesCS1A01G300600	chr5B	83.096	562	62	15	1214	1764	491280084	491280623	5.290000e-132	481.0
19	TraesCS1A01G300600	chr5B	87.770	417	39	8	1257	1666	491272800	491273211	6.840000e-131	477.0

These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

	query	scaffold	start	end	length	rev.comp	avg.bitscore	max.bitscore	avg.percent.identical	query.start	query.end	num_hsp	groupid	homo_length
0	TraesCS1A01G300600	chr1A	495331315	495334044	2729	False	5042	5042	100.000	1	2730	1	chr1A.!!$F2	2729
1	TraesCS1A01G300600	chr1D	398379575	398381437	1862	False	2510	2510	91.223	886	2730	1	chr1D.!!$F4	1844
2	TraesCS1A01G300600	chr1D	398246033	398246940	907	False	767	767	82.229	829	1765	1	chr1D.!!$F3	936
3	TraesCS1A01G300600	chr1D	398121325	398122091	766	False	702	702	83.544	889	1662	1	chr1D.!!$F2	773
4	TraesCS1A01G300600	chr1D	398093760	398094409	649	False	614	614	84.036	1116	1765	1	chr1D.!!$F1	649
5	TraesCS1A01G300600	chr1B	533815167	533816935	1768	False	2218	2218	89.418	942	2720	1	chr1B.!!$F3	1778
6	TraesCS1A01G300600	chr1B	26839775	26840609	834	True	1267	1267	94.139	1	831	1	chr1B.!!$R1	830
7	TraesCS1A01G300600	chr1B	533759781	533760539	758	False	667	667	82.772	973	1763	1	chr1B.!!$F2	790
8	TraesCS1A01G300600	chr1B	533747815	533748510	695	False	623	623	83.287	1112	1804	1	chr1B.!!$F1	692
9	TraesCS1A01G300600	chr7A	594889133	594889962	829	False	1303	1303	95.066	1	827	1	chr7A.!!$F1	826
10	TraesCS1A01G300600	chr7A	276127633	276128463	830	True	1299	1299	94.952	1	828	1	chr7A.!!$R1	827
11	TraesCS1A01G300600	chr7A	705060202	705061035	833	False	1284	1284	94.498	1	833	1	chr7A.!!$F2	832
12	TraesCS1A01G300600	chr7A	689968780	689969606	826	True	1277	1277	94.565	1	825	1	chr7A.!!$R2	824
13	TraesCS1A01G300600	chr2A	319016946	319017776	830	True	1288	1288	94.718	1	828	1	chr2A.!!$R1	827
14	TraesCS1A01G300600	chr2A	621443302	621444129	827	False	1277	1277	94.572	1	825	1	chr2A.!!$F1	824
15	TraesCS1A01G300600	chr3A	649848536	649849367	831	True	1279	1279	94.478	1	828	1	chr3A.!!$R1	827
16	TraesCS1A01G300600	chr6A	93180393	93181219	826	True	1271	1271	94.451	1	825	1	chr6A.!!$R1	824
17	TraesCS1A01G300600	chr5B	491280084	491280623	539	False	481	481	83.096	1214	1764	1	chr5B.!!$F2	550

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
765	769	0.107643	TGATGACTGGGCGTTTGTGA	59.892	50.0	0.0	0.0	0.0	3.58	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1772	1835	0.658536	GTGCTGCTTTCTCGTGTTGC	60.659	55.0	0.0	0.0	0.0	4.17	R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
163	164	1.186200	AGTCGGAGTAGAGCATGCAA	58.814	50.000	21.98	1.32	0.00	4.08
242	243	1.209898	CGCCGCTTTTCATTGCTCA	59.790	52.632	0.00	0.00	0.00	4.26
405	407	3.379445	CTCGGTGGGCGTGTACCT	61.379	66.667	0.00	0.00	34.77	3.08
622	626	5.333566	AAACCTTGACTTTTCCCCTATCA	57.666	39.130	0.00	0.00	0.00	2.15
746	750	1.202651	CGATTTTCGGCATCCTAGGGT	60.203	52.381	9.46	0.00	36.00	4.34
747	751	2.222027	GATTTTCGGCATCCTAGGGTG	58.778	52.381	18.47	18.47	0.00	4.61
749	753	1.507140	TTTCGGCATCCTAGGGTGAT	58.493	50.000	26.91	0.09	0.00	3.06
758	762	1.443407	CTAGGGTGATGACTGGGCG	59.557	63.158	0.00	0.00	0.00	6.13
759	763	1.305802	TAGGGTGATGACTGGGCGT	60.306	57.895	0.00	0.00	0.00	5.68
764	768	0.238289	GTGATGACTGGGCGTTTGTG	59.762	55.000	0.00	0.00	0.00	3.33
765	769	0.107643	TGATGACTGGGCGTTTGTGA	59.892	50.000	0.00	0.00	0.00	3.58
767	771	0.179032	ATGACTGGGCGTTTGTGACA	60.179	50.000	0.00	0.00	0.00	3.58
793	799	1.228429	CCGAAAAAGTGGCCTGGGA	60.228	57.895	3.32	0.00	0.00	4.37
876	883	4.790962	TGCCTAGCTGCAGCCTGC	62.791	66.667	34.39	30.71	45.29	4.85
878	885	3.795041	CCTAGCTGCAGCCTGCCT	61.795	66.667	34.39	18.55	44.23	4.75
879	886	2.514128	CTAGCTGCAGCCTGCCTG	60.514	66.667	34.39	14.41	44.23	4.85
925	934	2.646250	CGCCCTTTTTCAAAGTACACG	58.354	47.619	0.00	0.00	0.00	4.49
927	936	2.034179	GCCCTTTTTCAAAGTACACGCT	59.966	45.455	0.00	0.00	0.00	5.07
939	957	1.697082	TACACGCTCCCCCACAAACA	61.697	55.000	0.00	0.00	0.00	2.83
947	965	1.406065	CCCCCACAAACAATGGTGCA	61.406	55.000	0.00	0.00	35.23	4.57
980	998	3.069158	GCGTCCGCTTATATATACCCCAT	59.931	47.826	4.10	0.00	38.26	4.00
982	1000	4.500887	CGTCCGCTTATATATACCCCATGG	60.501	50.000	4.14	4.14	37.80	3.66
1033	1059	0.394762	GCTCCCACAGGCATCAATCA	60.395	55.000	0.00	0.00	0.00	2.57
1034	1060	1.753141	GCTCCCACAGGCATCAATCAT	60.753	52.381	0.00	0.00	0.00	2.45
1035	1061	2.228059	CTCCCACAGGCATCAATCATC	58.772	52.381	0.00	0.00	0.00	2.92
1050	1076	5.371526	TCAATCATCCAGTTCCAATAGCTC	58.628	41.667	0.00	0.00	0.00	4.09
1052	1080	2.103094	TCATCCAGTTCCAATAGCTCGG	59.897	50.000	0.00	0.00	0.00	4.63
1054	1082	1.757118	TCCAGTTCCAATAGCTCGGAG	59.243	52.381	0.00	0.00	31.51	4.63
1078	1106	2.107141	CCGGGCGAACTCATCTCC	59.893	66.667	0.00	0.00	31.73	3.71
1087	1115	2.224314	CGAACTCATCTCCGATCGATCA	59.776	50.000	24.40	5.92	32.38	2.92
1118	1150	3.429272	GGGCATCATCATCGATCTCTCTC	60.429	52.174	0.00	0.00	0.00	3.20
1134	1166	7.520453	CGATCTCTCTCCTCTCTGATTAACTTG	60.520	44.444	0.00	0.00	0.00	3.16
1225	1262	2.592287	GACCACGCCCACGGAAAA	60.592	61.111	0.00	0.00	46.04	2.29
1231	1268	2.750237	GCCCACGGAAAAGGCGAT	60.750	61.111	0.00	0.00	36.84	4.58
1233	1270	2.485122	CCACGGAAAAGGCGATGC	59.515	61.111	0.00	0.00	0.00	3.91
1486	1544	4.764771	TACGGGTCCGGGGAGGTG	62.765	72.222	14.25	0.00	44.69	4.00
1807	1870	2.045242	ACAGCTCTGCATGCCCAG	60.045	61.111	16.68	11.88	0.00	4.45
1809	1872	3.336568	AGCTCTGCATGCCCAGGT	61.337	61.111	16.68	13.34	33.64	4.00
1895	1964	2.536365	TCAACGTATGATCGAACTGCC	58.464	47.619	0.00	0.00	31.50	4.85
1900	1969	1.940613	GTATGATCGAACTGCCCAACC	59.059	52.381	0.00	0.00	0.00	3.77
1916	1985	4.036971	GCCCAACCGCACATGTAAATATTA	59.963	41.667	0.00	0.00	0.00	0.98
1945	2014	2.744202	CAGAACACTGTACTGGCAATCC	59.256	50.000	4.66	0.00	0.00	3.01
1950	2019	1.337823	ACTGTACTGGCAATCCGACAC	60.338	52.381	4.66	0.00	34.14	3.67
1955	2024	1.577328	CTGGCAATCCGACACACCAC	61.577	60.000	0.00	0.00	34.14	4.16
2353	2426	1.227380	GATTCAGGCATCCTCGCGT	60.227	57.895	5.77	0.00	0.00	6.01
2354	2427	1.493950	GATTCAGGCATCCTCGCGTG	61.494	60.000	5.77	2.75	46.51	5.34
2355	2428	4.819761	TCAGGCATCCTCGCGTGC	62.820	66.667	5.77	8.67	45.16	5.34
2426	2502	0.392461	GTTCAACCGCCTGGATGCTA	60.392	55.000	0.00	0.00	37.92	3.49
2427	2503	0.392461	TTCAACCGCCTGGATGCTAC	60.392	55.000	0.00	0.00	37.92	3.58
2428	2504	2.173669	CAACCGCCTGGATGCTACG	61.174	63.158	0.00	0.00	39.21	3.51
2429	2505	4.530857	ACCGCCTGGATGCTACGC	62.531	66.667	0.00	0.00	39.21	4.42
2508	2584	4.267928	CCTTTGCCGACTAAAACTATCTCG	59.732	45.833	0.00	0.00	0.00	4.04
2551	2634	0.405973	AGGAGGAAAAAGAGGCCACC	59.594	55.000	5.01	0.00	33.25	4.61
2608	2691	2.552743	TGGTGGCTCGATTACTCTATCG	59.447	50.000	0.00	0.00	46.63	2.92
2639	2722	5.107491	CCAACCATGAATCATCACGTATACG	60.107	44.000	23.24	23.24	46.33	3.06
2687	2770	4.201832	CGATCGGGTAAGATAAGATCCTCG	60.202	50.000	7.38	0.00	35.56	4.63
2707	2790	3.254654	CGAGCGTATGTGGCACCG	61.255	66.667	16.26	12.67	0.00	4.94

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
163	164	1.338337	CGACATCGTCTCCAAGGCTAT	59.662	52.381	0.00	0.00	34.11	2.97
227	228	1.973138	CTGGTGAGCAATGAAAAGCG	58.027	50.000	0.00	0.00	35.48	4.68
242	243	4.694233	CCTCGCACAGCTGCTGGT	62.694	66.667	31.00	15.43	41.77	4.00
445	447	2.519302	ACAGCAGCTGGGCGTTTT	60.519	55.556	26.38	0.00	39.27	2.43
498	500	0.472925	TAGATAGCCATTCCCCGCCA	60.473	55.000	0.00	0.00	0.00	5.69
680	684	1.227615	GGTCACAAACCGAACCCGA	60.228	57.895	0.00	0.00	38.58	5.14
746	750	0.107643	TCACAAACGCCCAGTCATCA	59.892	50.000	0.00	0.00	0.00	3.07
747	751	0.517316	GTCACAAACGCCCAGTCATC	59.483	55.000	0.00	0.00	0.00	2.92
749	753	0.813610	CTGTCACAAACGCCCAGTCA	60.814	55.000	0.00	0.00	0.00	3.41
758	762	4.683334	GCGCCGGCTGTCACAAAC	62.683	66.667	26.68	0.00	35.83	2.93
836	843	2.112718	GCTGCTGCAGGGATAGGG	59.887	66.667	29.05	4.36	39.41	3.53
887	894	3.737172	CTTCCCGGCCAAGTTGCG	61.737	66.667	2.24	0.00	0.00	4.85
902	909	2.691011	TGTACTTTGAAAAAGGGCGCTT	59.309	40.909	10.73	10.73	0.00	4.68
925	934	0.831711	ACCATTGTTTGTGGGGGAGC	60.832	55.000	0.00	0.00	41.14	4.70
927	936	1.118356	GCACCATTGTTTGTGGGGGA	61.118	55.000	0.00	0.00	40.60	4.81
961	979	3.389983	GCCATGGGGTATATATAAGCGGA	59.610	47.826	15.13	0.00	36.17	5.54
964	982	4.412199	TCTGGCCATGGGGTATATATAAGC	59.588	45.833	15.13	0.00	36.17	3.09
980	998	1.838396	TCACACTCTGCTCTGGCCA	60.838	57.895	4.71	4.71	37.74	5.36
982	1000	0.669932	CTGTCACACTCTGCTCTGGC	60.670	60.000	0.00	0.00	39.26	4.85
1033	1059	2.366916	CTCCGAGCTATTGGAACTGGAT	59.633	50.000	3.67	0.00	38.62	3.41
1034	1060	1.757118	CTCCGAGCTATTGGAACTGGA	59.243	52.381	3.67	0.00	38.62	3.86
1035	1061	1.808133	GCTCCGAGCTATTGGAACTGG	60.808	57.143	13.42	0.00	38.62	4.00
1078	1106	2.305853	CGCCCAGCTTGATCGATCG	61.306	63.158	20.03	9.36	0.00	3.69
1087	1115	4.133373	ATGATGCCCGCCCAGCTT	62.133	61.111	0.00	0.00	0.00	3.74
1118	1150	6.409704	TGGTTGATCAAGTTAATCAGAGAGG	58.590	40.000	8.80	0.00	34.76	3.69
1134	1166	1.823899	GGACGGCCCATGGTTGATC	60.824	63.158	11.73	2.91	34.14	2.92
1486	1544	3.887327	GCGCACACGTCGTCGATC	61.887	66.667	9.47	0.00	42.83	3.69
1697	1755	2.173669	CGGCGATCATTTCCGTGCT	61.174	57.895	0.00	0.00	38.47	4.40
1730	1791	2.395690	GTTGCGCGACGGATGAAG	59.604	61.111	12.10	0.00	0.00	3.02
1772	1835	0.658536	GTGCTGCTTTCTCGTGTTGC	60.659	55.000	0.00	0.00	0.00	4.17
1775	1838	1.502163	GCTGTGCTGCTTTCTCGTGT	61.502	55.000	0.00	0.00	0.00	4.49
1807	1870	1.000843	GAAAATGGTGCCACAAGGACC	59.999	52.381	0.00	0.00	36.89	4.46
1809	1872	1.337118	GGAAAATGGTGCCACAAGGA	58.663	50.000	0.00	0.00	36.89	3.36
1891	1960	1.240641	TTACATGTGCGGTTGGGCAG	61.241	55.000	9.11	0.00	44.93	4.85
1895	1964	6.427150	GTCTAATATTTACATGTGCGGTTGG	58.573	40.000	9.11	0.00	0.00	3.77
1900	1969	4.663140	CGCCGTCTAATATTTACATGTGCG	60.663	45.833	9.11	6.28	0.00	5.34
1916	1985	1.802337	TACAGTGTTCTGCGCCGTCT	61.802	55.000	4.18	0.00	44.77	4.18
1945	2014	1.257936	CTTTTCACTCGTGGTGTGTCG	59.742	52.381	10.04	0.00	45.50	4.35
1950	2019	2.851824	GCAAAACTTTTCACTCGTGGTG	59.148	45.455	0.00	5.25	46.60	4.17
1955	2024	3.691049	TCCAGCAAAACTTTTCACTCG	57.309	42.857	0.00	0.00	0.00	4.18
1960	2029	6.138088	GCAAATTGATCCAGCAAAACTTTTC	58.862	36.000	0.00	0.00	0.00	2.29
2226	2299	4.085204	TTATCCCGGCGGTTGCGT	62.085	61.111	26.32	8.04	44.10	5.24
2353	2426	3.646715	GCCACCCCCACTAGTGCA	61.647	66.667	17.86	0.00	32.48	4.57
2354	2427	4.426313	GGCCACCCCCACTAGTGC	62.426	72.222	17.86	3.90	32.48	4.40
2429	2505	1.149361	TTATTCAGCTAACCCGCGCG	61.149	55.000	25.67	25.67	34.40	6.86
2530	2613	2.163509	GTGGCCTCTTTTTCCTCCTTC	58.836	52.381	3.32	0.00	0.00	3.46
2551	2634	1.093972	TGCATATGTTTGCCACGGAG	58.906	50.000	4.29	0.00	42.06	4.63
2576	2659	2.202650	GCCACCAATCACGCATGC	60.203	61.111	7.91	7.91	0.00	4.06
2580	2663	1.369091	AATCGAGCCACCAATCACGC	61.369	55.000	0.00	0.00	0.00	5.34
2608	2691	2.524306	TGATTCATGGTTGGGTGGTTC	58.476	47.619	0.00	0.00	0.00	3.62
2639	2722	0.788391	GACCGTCCAATCAACACGAC	59.212	55.000	0.00	0.00	35.49	4.34
2641	2724	2.259618	CTAGACCGTCCAATCAACACG	58.740	52.381	0.00	0.00	0.00	4.49
2642	2725	2.000447	GCTAGACCGTCCAATCAACAC	59.000	52.381	0.00	0.00	0.00	3.32
2695	2778	1.067212	CTCCTAGACGGTGCCACATAC	59.933	57.143	0.00	0.00	0.00	2.39
2707	2790	2.032675	CCTAACGCGGTAACTCCTAGAC	59.967	54.545	12.47	0.00	0.00	2.59

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.